Genome editing technology and applications with the type I CRISPR system

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, which are representative genome editing technologies, are classified into class 1 and class 2 in terms of evolutionary biology and are further classified into several subtypes. Class 2 CRISPR systems, including type II Cas9 and type V Cas12a, are the most commonly used for genome editing in eukaryotic cells, while type I CRISPR systems within Class 1 are also becoming available. Type I CRISPR recognizes longer target sequences than CRISPR-Cas9 and can induce large deletion mutations of several kilobases. These features demonstrate its potential as a novel and unique genome editing tool that can induce genetic disruption safely and reliably. Thus, it is expected to be utilized for gene therapy and industrial applications. Recently, the DNA cleavage mechanism of type I CRISPR has also revealed details from protein-complex analyses with X-ray crystallography, cryo-electron microscopy, and high-speed atomic force microscopy. The single-strand DNA trans-cleavage activity of type I CRISPR, called collateral activity, has broadened the potential application for CRISPR diagnostics, especially in the development of point-of-care testing methods for COVID-19. In this review, we present an overview of the type I CRISPR system, its application to genome editing, and genetic diagnosis using CRISPR-Cas3.Copyright © 2022

Mutagenicity of N-Hydroxycytidine and Monlnupiravir in E. Coli and Mammalian Cell Cultures

Molnupiravir (MOV) has received FDA's Emergency Use Authorization for the treatment of COVID-19, which is caused by SARS-CoV-2 infection. MOV is a prodrug of the ribonucleoside analog, Nhydroxycytidine (NHC). Upon phosphorylation, NHC incorporates into nascent viral RNA during replication triggering “catastrophic” mutation of the viral genome. However, NHC can also enter the deoxy-ribonucleotide pool, become incorporated into DNA, and cause DNA mutations. In nonclinical safety assessments, MOV was positive (i.e., mutagenic) in the Ames assay but negative in regulatory in vitro and in vivo micronucleus assays. Multiple in vitro studies conducted in bacteriophages, bacteria, fungi, and mammalian cells have reported that NHC can induce DNA mutations, mainly A:T>G:C transitions. We used a recently developed error-corrected wholegenome sequencing technique for detecting mutations induced by MOV and NHC in cultures of E. coli, mouse L5178YTk+/-, and human TK6 cells. Treatment of bacterial and mammalian cultures (for 4 hours and 5 days, respectively) with either MOV or NHC increased mutation frequencies in a dose-dependent manner in all three models. The majority of induced mutations were A:T>G:C, consistent with the type of mutation caused by incorporation of dNHC opposite to dA in the first round of DNA replication and incorporation of dG opposite to dNHC in the subsequent round(s) of DNA replication. Trinucleotide mutational signatures in MOV/NHC-treated cells were similar in mouse and human cells and different from the background spontaneous mutational signatures in parental cell cultures. The specific mutational signature was evident in mammalian cells exposed to NHC concentrations comparable to those observed in the plasma of human subjects who received clinical doses of MOV. This data indicates more well-controlled rodent and clinical studies of MOV/NHC-induced mutagenicity should be done in the interest of public health safety.

The development of a novel SARS-CoV-2 virus neutralizing immunotoxin

For decades, scientific efforts were focused on the improvement of the effectiveness of the therapeutic antibodies, mainly in order reduce the dosage and thus lower the side-effects and costs. P4A1, a potent SARS-CoV-2 virus neutralizing antibody was already engineered to contain Fc fragment mutations, that dramatically increased the blood circulation time. In this work, we aimed to further enhance this neutralizing antibody efficacy by creating a next-generation virus neutralizing agent based on the P4A1 and conjugated with a highly processive Bacillus amyloliquefaciens RNase (barnase). Barnase itself is known to act as a mild toxin that drives the cells to apoptosis, and we propose that its RNase activity may enhance the protective effect through the hydrolysis of viral RNA in infected cells, and thereby additionally preventing pathogen replication. The main challenge in the assembly of such molecule is the intrinsic barnase toxicity in mammalian cells, what precludes the possibility to express it as a fusion protein. Further, we had shown that barnase, being a small (12.5 kDa) protein, contains very few surface reactive moieties that are available for conventional chemical crosslinking strategies. Therefore, the antibody-barnase fusion protein was obtained by enzymatic conjugation via the sortase A enzyme. The reaction conditions for bacterially expressed barnase and HEK293 derived P4A1 modified to contain heavy chain C-terminal sortase motif were thoroughly optimized and the reaction yield approached 80%. The immunotoxin RBD binding EC50 was not found to differ from the unconjugated P4A1 antibody and barnase activity was found to be 33% of the one for unmodified enzyme. Thus, we obtained the promising immunotoxin with a good yield, which had retained its RNase activity for the further in vitro virus neutralization studies.

DEVELOPMENT of COVID-19 MONOCLONAL ANTIBODIES and RECOMBINANT PROTEINS AS REAGENTS for BIOMEDICAL RESEARCH and DIAGNOSTIC TESTS

Since SARS-COV-2 virus spread worldwide and COVID-19 turned rapidly into a pandemic illness, the necessity for vaccines and diagnostic tests became crucial. The viral surface is decorated with Spike, the major antigenic determinant and main target for vaccine development. Within Spike, the receptor binding domain (RBD), constitutes the main target of highly neutralizing antibodies found in COVID-19 convalescent plasma. Besides vaccination, another important aspect of Spike (and RBD) is their use as immunogen for the development of poli- and monoclonal antibodies (mAbs) for therapeutic and diagnostic purposes. Here we report the development and preliminary biochemical characterization of a set of monoclonal antibodies against the Spike RBD domain along with the recombinant expression of two mayor COVID-19 protein reagents: the viral Spike RBD domain and the extracellular domain of the human receptor ACE2. RBD and the extracellular domain of ACE2 (aa 1-740) were obtained through transient gene transfection (TGE) in two different mammalian cell culture systems: HEK293T adherent monolayers and Expi293F™ suspension cultures. Due to its low cost and ease scale-up, all transfections were carried with polyethyleneimine (PEI). Expressed proteins were purified from culture supernatants by immobilized metal affinity chromatography. Anti-RBD mAbs were developed from two different immunization schemes: one aimed to elicit antibodies with viral neutralizing potential, and the other with the ability to recognize denatured RBD for routine lab immunoassays. To achieve this, the first group of mice was immunized with RBD in aluminum salts (RBD/Al) and the other with RBD emulsified in Freunds adjuvant (RBD/FA). Polyclonal and monoclonal antibody reactivities against native or denatured RBD forms were then assessed by ELISA. Complete RBD denaturation was followed by intrinsic fluorescence spectral changes upon different physicochemical stress treatments. As expected, RBD/Al immunized mice developed an antibody response shifted to native RBD while those immunized with RBD/FA showed a high response against both forms of the protein. In accordance with the observed polyclonal response, RBD/FA derived mAbs recognize both, native and denatured RBD. On the contrary, hybridomas generated from the RBD/Al protocol mostly recognize RBD in its native state. Further ELISA binding assays revealed that all RBD/FA derived mAbs can form a trimeric complex with ACE2 and RBD, denoting they would not have viral neutralizing activity. ELISA competition assays with the RBD/ACE2 complex aimed to determine the neutralization potential of the RBD/Al derived mAbs are under way. Overall, the anti-Spike RBD mAbs and the recombinant RBD and ACE2 proteins presented here constitute valuable tools for diverse COVID-19 academic research projects and local immunity surveillance testing.